The 204 complete genomic sequences of Plum pox virus in Genbank (Jan 2019) were downloaded. Their main ORFs were compared by phylogenetic and population genetic methods. All fell into the nine previously recognized strain clusters; the Rec and T strain ORFs were all recombinants, whereas most of those from the C, CR, CV, D, EA, M and W strain clusters were not. The strain clusters ranged in size from two (CV and EA) to 74 (D). Isolates of eight of the nine strains came, with an exception resulting from a quarantine breach, only from Europe and the Levant, but many D strain isolates also came from east and south Asia and the Americas. The estimated TMRCA of all 132 non-recombinant ORFs was 820 (865-775) BCE. Most strain populations were only a few decades old, and had small intra-strain, but large inter-strain, differences; strain W was older. Europe is clearly the ‘centre of emergence’ of PPV, and the several D strain populations found elsewhere show evidence of gene flow only with Europe, so have come from separate introductions from Europe. All ORFs and their individual genes show evidence of strong negative selection, except the positively selected PIPO gene of the recently migrant populations. The possible ancient origins of PPV are discussed.
